As we have experienced you can not stack embarked military units with ships. You can only have a ship traveling nearby the unit. But this does not protect it from being killed by enemy ship coming outside the fog of war. Even if you dominate the sea you can not ensure unit coming to the enemy shore alive.
I have played islands game and AI killed half of my land invasion forces just with 2 caravels, I had 4 frigates traveling not far from them. Zones of control do not work. Unless you play Songhai your transport fleet will always be defendless